vcf格式解析源文件pdf 结构变异中，在INFO列可以看到变异类型 SVTYPE=BND 5.4 Specifying complex rearrangements with breakends An arbitrary rearrangement event can be summarized as a set of novel adjacencies. Each adjacency ties together 2 breakends. The two breakends at either end of a novel adjacency are called mates. There is one line of VCF (i.e. one record) for each of the two breakends in a novel adjacency. A breakend record is identified with the tag “SYTYPE=BND” in the INFO field. The REF field of a breakend record indicates a base or sequence s of bases beginning at position POS, as in all VCF records. The ALT field of a breakend record indicates a replacement for s. This “breakend replacement” has three parts: 1. The string t that replaces places s. The string t may be an extended version of s if some novel bases are inserted during the formation of the novel adjacency. 2. The position p of the mate breakend, indicated by a string of the form “chr:pos”. This is the location of the first mapped base in the piece being joined at this novel adjacency. 3. The direction that the joined sequence continues in, starting from p. This is indicated by the orientation of square brackets surrounding p. These 3 elements are combined in 4 possible ways to create the ALT. In each of the 4 cases, the assertion is that s is replaced with t, and then some piece starting at position p is joined to t. The cases are: REF ALT Meaning s t[p[ piece extending to the right of p is joined after t s t]p] reverse comp piece extending left of p is joined after t s ]p]t piece extending to the left of p is joined before t s [p[t reverse comp piece extending right of p is joined before t The example in Figure 1 shows a 3-break operation involving 6 breakends. It exemplifies all possible orientations of breakends in adjacencies. Notice how the ALT field expresses the orientation of the breakends.

CHROM POS ID REF ALT QUAL FILTER INFO

2 321681 bnd W G G]17:198982] 6 PASS SVTYPE=BND 2 321682 bnd V T ]13:123456]T 6 PASS SVTYPE=BND 13 123456 bnd U C C[2:321682[ 6 PASS SVTYPE=BND 13 123457 bnd X A [17:198983[A 6 PASS SVTYPE=BND 17 198982 bnd Y A A]2:321681] 6 PASS SVTYPE=BND 17 198983 bnd Z C [13:123457[C 6 PASS SVTYPE=BND